Zobrazeno 1 - 10
of 21
pro vyhledávání: '"Martin, Culka"'
Autor:
Michal Tupec, Martin Culka, Aleš Machara, Stanislav Macháček, Daniel Bím, Aleš Svatoš, Lubomír Rulíšek, Iva Pichová
Publikováno v:
Computational and Structural Biotechnology Journal, Vol 20, Iss , Pp 1378-1388 (2022)
A recently proposed reaction mechanism of soluble Δ9 desaturase (Δ9D) allowed us to identify auxiliary residues His203, Asp101, Thr206 and Cys222 localized near the di-iron active site that are supposedly involved in the proton transfer (PT) to and
Externí odkaz:
https://doaj.org/article/47cf60acbf0b4ad0a35769b2f757cb87
Autor:
Oldřich Hudeček, Roberto Benoni, Paul E. Reyes-Gutierrez, Martin Culka, Hana Šanderová, Martin Hubálek, Lubomír Rulíšek, Josef Cvačka, Libor Krásný, Hana Cahová
Publikováno v:
Nature Communications, Vol 11, Iss 1, Pp 1-11 (2020)
Nicotinamide adenine dinucleotide and coenzyme A serve as a 5′-cap of prokaryotic RNA. Here the authors report that methylated and non-methylated dinucleoside polyphosphates (Np n Ns) exist as Escherichia coli RNA caps which can be cleaved by 5′-
Externí odkaz:
https://doaj.org/article/a626bb909a284b82ac5da5fc2819c265
Autor:
Christina Diederich, Mario Leypold, Martin Culka, Hansjörg Weber, Rolf Breinbauer, G. Matthias Ullmann, Wulf Blankenfeldt
Publikováno v:
Scientific Reports, Vol 7, Iss 1, Pp 1-13 (2017)
Abstract Phenazines are bacterial virulence and survival factors with important roles in infectious disease. PhzF catalyzes a key reaction in their biosynthesis by isomerizing (2 S,3 S)-2,3-dihydro-3-hydroxy anthranilate (DHHA) in two steps, a [1,5]-
Externí odkaz:
https://doaj.org/article/2067ab1830ad4e8891977558d2293393
Autor:
Daniel Bím, Michal Navrátil, Ondrej Gutten, Jan Konvalinka, Zsófia Kutil, Martin Culka, Václav Navrátil, Anastassia N. Alexandrova, Cyril Bařinka, Lubomír Rulíšek
Publikováno v:
The Journal of Physical Chemistry B. 126:132-143
Quantum and molecular mechanics (QM/MM) and QM-only (cluster model) modeling techniques represent the two workhorses in mechanistic understanding of enzyme catalysis. One of the stringent tests for QM/MM and/or QM approaches is to provide quantitativ
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::41362eb0c51b8444cb2511c8f700512b
https://doi.org/10.1021/acs.jpcb.1c09240
https://doi.org/10.1021/acs.jpcb.1c09240
Publikováno v:
The journal of physical chemistry. B. 126(32)
We extensively mapped energy landscapes and conformations of 22 (including three His protonation states) proteinogenic α-amino acids in
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f8d0ce0467c93721f558226e91b99c93
https://pubmed.ncbi.nlm.nih.gov/35930560
https://pubmed.ncbi.nlm.nih.gov/35930560
Publikováno v:
ACS Chemical Biology. 15:1765-1772
Dinucleoside polyphosphates (NpnNs) were discovered 50 years ago in all cells. They are often called alarmones, even though the molecular target of the alarm has not yet been identified. Recently, we showed that they serve as noncanonical initiating
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d6c0c79f64ff799fdec6ac0c6eb17daf
https://doi.org/10.1021/acschembio.0c00178
https://doi.org/10.1021/acschembio.0c00178
Publikováno v:
Journal of the American Chemical Society. 142:10412-10423
A full understanding of the catalytic action of non-heme iron (NHFe) and non-heme diiron (NHFe2) enzymes is still beyond the grasp of contemporary computational and experimental techniques. Many of these enzymes exhibit fascinating chemo-, regio-, an
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::8b1394a3ff5f6093c374d94db834e35b
https://doi.org/10.1021/jacs.0c01786
https://doi.org/10.1021/jacs.0c01786
Autor:
Lubomír Rulíšek, Martin Culka
Publikováno v:
The Journal of Physical Chemistry B. 124:3252-3260
By computing strain energies of peptide fragments within protein structures and their intramolecular interaction energies, we attempt to reveal general biophysical trends behind the secondary structure formation in the context of protein evolution. O
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::469b78c43b924e7f325bd5d61095f34d
https://doi.org/10.1021/acs.jpcb.9b11784
https://doi.org/10.1021/acs.jpcb.9b11784
Autor:
Ioannis Kipouros, Agnieszka Stańczak, Martin Culka, Erik Andris, Timothy R. Machonkin, Lubomír Rulíšek, Edward I. Solomon
Publikováno v:
Chem Commun (Camb)
The factors that control the diverse reactivity of the μ-η(2):η(2)-peroxo dicopper(II) oxy-intermediates in the coupled binuclear copper proteins remain elusive. Here, spectroscopic and computational methods reveal H-bonding interactions between a
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f9e9f5e3127bac488e404092c28976c8
https://europepmc.org/articles/PMC8966618/
https://europepmc.org/articles/PMC8966618/
Publikováno v:
The Journal of Physical Chemistry B. 123:1215-1227
By combining bioinformatics with quantum-chemical calculations, we attempt to address quantitatively some of the physical principles underlying protein folding. The former allowed us to identify tripeptide sequences in existing protein three-dimensio
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2fc8e6638d842a888ad44b4697c19088
https://doi.org/10.1021/acs.jpcb.8b09245
https://doi.org/10.1021/acs.jpcb.8b09245